vg::GAFOutputCaller Class Reference

#include <graph_caller.hpp>

Inheritance diagram for vg::GAFOutputCaller:

Public Member Functions
	GAFOutputCaller (AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding)
	The emitter object is created and owned by external forces. More...
virtual	~GAFOutputCaller ()
void	emit_gaf_traversals (const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)
	print the GAF traversals More...
void	emit_gaf_variant (const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, const vector< int > &genotype, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)
	print the GAF genotype More...
SnarlTraversal	pad_traversal (const PathHandleGraph &graph, const SnarlTraversal &trav) const
	pad a traversal with (first found) reference path, adding up to trav_padding to each side More...

Protected Attributes
AlignmentEmitter *	emitter
string	gaf_sample_name
	Sample name. More...
size_t	trav_padding = 0
unordered_set< string >	ref_paths
	Reference paths are used to pad out traversals. If there are none, then first path found is used. More...

Detailed Description

Helper class for outputing snarl traversals as GAF

Constructor & Destructor Documentation

GAFOutputCaller()

vg::GAFOutputCaller::GAFOutputCaller	(	AlignmentEmitter *	emitter,
		const string &	sample_name,
		const vector< string > &	ref_paths,
		size_t	trav_padding
	)

The emitter object is created and owned by external forces.

~GAFOutputCaller()

vg::GAFOutputCaller::~GAFOutputCaller ( )

virtual

Member Function Documentation

emit_gaf_traversals()

void vg::GAFOutputCaller::emit_gaf_traversals	(	const PathHandleGraph &	graph,
		const string &	snarl_name,
		const vector< SnarlTraversal > &	travs,
		int64_t	ref_trav_idx,
		const string &	ref_path_name,
		int64_t	ref_path_position,
		const TraversalSupportFinder *	support_finder = nullptr
	)

print the GAF traversals

emit_gaf_variant()

void vg::GAFOutputCaller::emit_gaf_variant	(	const PathHandleGraph &	graph,
		const string &	snarl_name,
		const vector< SnarlTraversal > &	travs,
		const vector< int > &	genotype,
		int64_t	ref_trav_idx,
		const string &	ref_path_name,
		int64_t	ref_path_position,
		const TraversalSupportFinder *	support_finder = nullptr
	)

print the GAF genotype

pad_traversal()

SnarlTraversal vg::GAFOutputCaller::pad_traversal	(	const PathHandleGraph &	graph,
		const SnarlTraversal &	trav
	)		const

pad a traversal with (first found) reference path, adding up to trav_padding to each side

Member Data Documentation

emitter

AlignmentEmitter* vg::GAFOutputCaller::emitter

protected

gaf_sample_name

string vg::GAFOutputCaller::gaf_sample_name

protected

Sample name.

ref_paths

unordered_set<string> vg::GAFOutputCaller::ref_paths

protected

Reference paths are used to pad out traversals. If there are none, then first path found is used.

trav_padding

size_t vg::GAFOutputCaller::trav_padding = 0

protected

Add padding from reference paths to traversals to make them at least this long (only in emit_gaf_traversals(), not emit_gaf_variant)

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The documentation for this class was generated from the following files:

• src/graph_caller.hpp
• src/graph_caller.cpp